Variant report

Variant	rs6693384
Chromosome Location	chr1:45530572-45530573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45284099..45286041-chr1:45529730..45532603,2	K562	blood:
2	chr1:45524312..45527029-chr1:45527867..45530740,2	K562	blood:

Variant related genes	Relation type
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10127477	1.00[AMR][1000 genomes]
rs10127522	1.00[AMR][1000 genomes]
rs10128015	0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11801715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802325	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13373924	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13374526	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13374751	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13374976	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13376626	0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13376629	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28430778	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6659393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6663316	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6665506	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6665903	1.00[AMR][1000 genomes]
rs6665943	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6689406	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6702757	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7516271	0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7521226	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7550194	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv945714	chr1:45529328-45533650	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6693384	FAM49A	trans	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45524600-45532800	Weak transcription	Brain Substantia Nigra	brain
2	chr1:45525200-45534600	Weak transcription	Brain Angular Gyrus	brain
3	chr1:45525800-45558600	Weak transcription	HepG2	liver
4	chr1:45526200-45532000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:45526600-45532400	Weak transcription	Ovary	ovary

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